Variant report

Variant	rs2313602
Chromosome Location	chr1:228331040-228331041
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228327114-228332328	IMR90	lung:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228267667..228275106-chr1:228326600..228331394,10	K562	blood:
2	chr1:228328826..228331169-chr1:228395338..228396936,2	K562	blood:
3	chr1:228284520..228292111-chr1:228324853..228335412,14	K562	blood:
4	chr1:228329673..228331398-chr1:228643962..228646150,2	K562	blood:
5	chr1:228326053..228331395-chr1:228462710..228467617,6	K562	blood:
6	chr1:228328463..228331528-chr1:228462308..228464210,3	K562	blood:
7	chr1:228295402..228297803-chr1:228330568..228332279,2	MCF-7	breast:
8	chr1:228293945..228298682-chr1:228326047..228331152,9	K562	blood:

No data

Variant related genes	Relation type
GUK1	TF binding region
ENSG00000154358	Chromatin interaction
ENSG00000162910	Chromatin interaction
ENSG00000269934	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000264944	Chromatin interaction
ENSG00000143793	Chromatin interaction
ENSG00000181218	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10158357	0.84[CEU][hapmap]
rs1059778	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10753445	0.83[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs10799468	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10799469	0.84[EUR][1000 genomes]
rs10799471	0.83[EUR][1000 genomes]
rs10916265	0.88[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10916268	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916271	0.95[EUR][1000 genomes]
rs11584385	1.00[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs11799681	0.83[EUR][1000 genomes]
rs11804508	0.85[EUR][1000 genomes]
rs12024649	0.84[EUR][1000 genomes]
rs12084338	0.84[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs12118872	0.91[CEU][hapmap]
rs12130630	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs12134624	0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs12564763	1.00[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12726781	0.85[EUR][1000 genomes]
rs12745416	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1331303	0.80[EUR][1000 genomes]
rs1411910	1.00[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs1557026	0.84[CEU][hapmap]
rs1620111	1.00[CEU][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs1629290	0.80[EUR][1000 genomes]
rs1629294	0.82[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.83[LWK][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs1745417	0.86[CHB][hapmap]
rs1745423	0.87[TSI][hapmap]
rs1757129	0.81[EUR][1000 genomes]
rs1757132	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1757133	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1757139	0.82[ASW][hapmap];1.00[CEU][hapmap];0.86[LWK][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs1757140	0.81[EUR][1000 genomes]
rs1757141	0.81[EUR][1000 genomes]
rs1757144	0.81[EUR][1000 genomes]
rs1757145	0.82[EUR][1000 genomes]
rs1757147	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1757148	0.82[EUR][1000 genomes]
rs1757149	0.81[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.86[LWK][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs1757150	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1757151	0.82[EUR][1000 genomes]
rs1757152	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.83[LWK][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs1757155	0.81[EUR][1000 genomes]
rs1757156	0.88[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.86[LWK][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs1757158	0.82[EUR][1000 genomes]
rs17640616	0.84[CEU][hapmap];0.87[TSI][hapmap]
rs1771459	1.00[CEU][hapmap];0.80[GIH][hapmap];0.81[EUR][1000 genomes]
rs1771460	0.88[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];0.86[LWK][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs1771461	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1771462	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1771467	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1771469	0.81[EUR][1000 genomes]
rs1771470	0.80[EUR][1000 genomes]
rs1771471	0.81[EUR][1000 genomes]
rs1771472	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1771474	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.83[LWK][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs1771476	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1771477	0.81[EUR][1000 genomes]
rs1771478	0.81[EUR][1000 genomes]
rs1771479	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1771482	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.83[LWK][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs1771483	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1771484	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs1771485	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1771487	0.96[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs2066237	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs2185544	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2298014	0.81[EUR][1000 genomes]
rs2313601	1.00[CEU][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs2776845	0.81[EUR][1000 genomes]
rs2776853	0.84[EUR][1000 genomes]
rs2776855	1.00[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2776856	0.88[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];0.86[LWK][hapmap];0.88[TSI][hapmap]
rs2792984	0.82[EUR][1000 genomes]
rs2872538	1.00[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs3094912	0.86[CHB][hapmap]
rs3094913	0.86[CHB][hapmap]
rs3094914	0.86[CHB][hapmap]
rs3121191	0.83[EUR][1000 genomes]
rs3121192	0.84[EUR][1000 genomes]
rs3795777	0.80[EUR][1000 genomes]
rs3795782	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs4653536	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4653543	0.80[EUR][1000 genomes]
rs4653907	0.81[EUR][1000 genomes]
rs4653915	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653917	0.84[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs4653919	0.81[EUR][1000 genomes]
rs4653920	0.81[EUR][1000 genomes]
rs4653921	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs4653931	0.81[EUR][1000 genomes]
rs493945	0.96[CEU][hapmap];0.85[TSI][hapmap]
rs55873533	0.81[EUR][1000 genomes]
rs55971985	0.85[EUR][1000 genomes]
rs56112646	0.81[EUR][1000 genomes]
rs61827540	0.81[EUR][1000 genomes]
rs6426492	0.81[CEU][hapmap]
rs6657968	0.84[CEU][hapmap]
rs6673893	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs6682260	0.84[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs708111	0.81[CHB][hapmap]
rs708112	0.82[CHB][hapmap]
rs708114	0.82[CHB][hapmap]
rs72757811	0.83[EUR][1000 genomes]
rs72757812	0.81[EUR][1000 genomes]
rs7512209	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7532924	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7537636	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7539762	0.84[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs849749	0.85[TSI][hapmap]
rs947087	1.00[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs964941	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
4	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
5	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
6	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
8	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
9	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
10	nsv873256	chr1:228322826-228359775	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
11	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
12	nsv549288	chr1:228327659-228363750	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
13	nsv549289	chr1:228327999-228371098	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2313602	IBA57	cis	Whole Blood	GTEx
rs2313602	OBSCN	cis	Esophagus Mucosa	GTEx
rs2313602	MRPL55	cis	cerebellum	SCAN
rs2313602	WDR26	cis	cerebellum	SCAN
rs2313602	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228328800-228332000	Enhancers	Fetal Brain Male	brain
2	chr1:228329000-228332000	Enhancers	Fetal Heart	heart
3	chr1:228329000-228332200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:228329000-228336800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:228329000-228339400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:228329000-228339600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:228329200-228331600	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
8	chr1:228329200-228331800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:228329200-228332600	Enhancers	Placenta Amnion	Placenta Amnion
10	chr1:228329200-228337400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:228329400-228331200	Flanking Active TSS	HepG2	liver
12	chr1:228329400-228333200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:228329400-228333800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:228329400-228333800	Genic enhancers	Spleen	Spleen
15	chr1:228329400-228336600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:228329400-228337600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:228329400-228337600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:228329400-228338200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:228329600-228331400	Enhancers	Psoas Muscle	Psoas
20	chr1:228329600-228331600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:228329600-228332000	Enhancers	Primary B cells from cord blood	blood
22	chr1:228329600-228332800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:228329600-228335200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:228329600-228335600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:228329600-228336800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:228329800-228331200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr1:228329800-228331600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:228329800-228331800	Enhancers	Brain Substantia Nigra	brain
29	chr1:228329800-228331800	Genic enhancers	Fetal Brain Female	brain
30	chr1:228329800-228332200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:228329800-228332200	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr1:228329800-228332600	Enhancers	Brain Anterior Caudate	brain
33	chr1:228329800-228332800	Enhancers	Liver	Liver
34	chr1:228329800-228336400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:228329800-228336600	Weak transcription	A549	lung
36	chr1:228330000-228332000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:228330000-228332000	Enhancers	Primary T cells fromperipheralblood	blood
38	chr1:228330000-228332000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:228330000-228332000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:228330000-228332000	Genic enhancers	Brain Germinal Matrix	brain
41	chr1:228330000-228332200	Enhancers	Right Atrium	heart
42	chr1:228330000-228332600	Enhancers	Primary T cells from cord blood	blood
43	chr1:228330000-228332600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr1:228330000-228332600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:228330000-228332600	Enhancers	Left Ventricle	heart
46	chr1:228330000-228332600	Enhancers	Stomach Mucosa	stomach
47	chr1:228330000-228332800	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr1:228330000-228333200	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr1:228330000-228333600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr1:228330000-228334800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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